6-87472969-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000369556(SLC35A1):c.-35C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000216 in 615,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00024 ( 0 hom. )
Consequence
SLC35A1
ENST00000369556 5_prime_UTR
ENST00000369556 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.519
Genes affected
SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 6-87472969-C-T is Benign according to our data. Variant chr6-87472969-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 383493.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152186Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000345 AC: 4AN: 11578Hom.: 0 AF XY: 0.000338 AC XY: 2AN XY: 5918
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GnomAD4 exome AF: 0.000240 AC: 111AN: 463308Hom.: 0 Cov.: 6 AF XY: 0.000230 AC XY: 56AN XY: 243060
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GnomAD4 genome AF: 0.000145 AC: 22AN: 152186Hom.: 0 Cov.: 34 AF XY: 0.0000807 AC XY: 6AN XY: 74354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 21, 2018
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at